4H4K | pdb_00004h4k

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

PDB DOI: https://doi.org/10.2210/pdb4H4K/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-17 Released: 2013-03-06
Deposition Author(s): Shao, Y., Cocozaki, A.I., Ramia, N.F., Terns, R.M., Terns, M.P., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.284 (Depositor), 0.272 (DCC)
R-Value Work:
0.214 (Depositor), 0.234 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the cmr2-cmr3 subcomplex of the cmr RNA silencing complex.

Shao, Y., Cocozaki, A.I., Ramia, N.F., Terns, R.M., Terns, M.P., Li, H.

(2013) Structure 21: 376-384

PubMed: 23395183 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2013.01.002
Primary Citation Related Structures:
4H4K

PubMed Abstract:
The Cmr complex is an RNA-guided effector complex that cleaves invader RNA in the prokaryotic immune response mediated by the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas system. Here, we report the crystal structure of a Cmr subcomplex containing Cmr2 (Cas10) and Cmr3 subunits at 2.8 Å resolution. The structure revealed a dual ferredoxin fold and glycine-rich loops characteristic of previously known repeat-associated mysterious proteins and two unique insertion elements in Cmr3 that mediate its interaction with Cmr2. Surprisingly, while mutation of both insertion elements significantly weakened Cmr3-Cmr2 interaction, they exhibit differential effects on Cmr-mediated RNA cleavage by the Cmr complex, suggesting stabilization of Cmr2-Cmr3 interactions by other subunits. Further mutational analysis of the two conserved (but non-Cmr2-binding) glycine-rich loops of Cmr3 identified a region that is likely involved in assembly or the RNA cleavage function of the Cmr complex.

Organizational Affiliation

Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.

Macromolecule Content

Total Structure Weight: 117.45 kDa
Atom Count: 7,014
Modeled Residue Count: 863
Deposited Residue Count: 1,018
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cmr subunit Cmr3	A	322	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: cmr3, PF1128
UniProt
Find proteins for Q8U1S7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1S7 Go to UniProtKB: Q8U1S7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U1S7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cmr subunit Cmr2	B [auth C]	696	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: cmr2, PF1129
UniProt
Find proteins for Q8U1S6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1S6 Go to UniProtKB: Q8U1S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U1S6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C MOL2 format, chain C mmCIF format, chain C	C	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C Interactions & Density Focus chain C
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	E [auth C], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284 (Depositor), 0.272 (DCC)
R-Value Work: 0.214 (Depositor), 0.234 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.523	α = 90
b = 135.958	β = 90
c = 189.655	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2013-03-27
Changes: Database references
Version 1.2: 2016-03-30
Changes: Other
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations