6YFV | pdb_00006yfv

Crystal structure of Mtr4-Red1 minimal complex from Chaetomium thermophilum

• PDB DOI: https://doi.org/10.2210/pdb6YFV/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermochaetoides thermophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-26 Released: 2021-05-05 
• Deposition Author(s): Dobrev, N., Ahmed, Y.L., Sinning, I.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain.

Dobrev, N., Ahmed, Y.L., Sivadas, A., Soni, K., Fischer, T., Sinning, I.

(2021) Nat Commun 12: 3456-3456

• PubMed: 34103492 
• DOI: https://doi.org/10.1038/s41467-021-23565-3
• Primary Citation Related Structures: 
  6YFV, 6YGU


• PubMed Abstract: 
  

  Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr4 and specific adaptor complexes for RNA substrate recognition. The PAXT and MTREC complexes have recently been identified as homologous exosome adaptors in human and fission yeast, respectively. The eleven-subunit MTREC comprises the zinc-finger protein Red1 and the Mtr4 homologue Mtl1. Here, we use yeast two-hybrid and pull-down assays to derive a detailed interaction map. We show that Red1 bridges MTREC submodules and serves as the central scaffold. In the crystal structure of a minimal Mtl1/Red1 complex an unstructured region adjacent to the Red1 zinc-finger domain binds to both the Mtl1 KOW domain and stalk helices. This interaction extends the canonical interface seen in Mtr4-adaptor complexes. In vivo mutational analysis shows that this interface is essential for cell survival. Our results add to Mtr4 versatility and provide mechanistic insights into the MTREC complex.

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Organizational Affiliation: 
• Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany. [e-mail].
The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia. [e-mail].
Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.62 kDa 
• Atom Count: 4,599 
• Modeled Residue Count: 569 
• Deposited Residue Count: 604 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP dependent RNA helicase (Dob1)-like protein	A, C	213	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: CTHT_0001850
UniProt
Find proteins for G0RZ64 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RZ64  Go to UniProtKB:  G0RZ64

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Red1	B, D	89	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: CTHT_0014920
UniProt
Find proteins for G0S1V1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S1V1  Go to UniProtKB:  G0S1V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN	E [auth B], G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.186	α = 90
b = 172.186	β = 90
c = 145.078	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
SHELXDE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Dobrev, N., Ahmed, Y.L., Sinning, I.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2021-06-23
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Refinement description, Structure summary