Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 90.11 kDa 
• Atom Count: 6228 
• Modelled Residue Count: 736 
• Deposited Residue Count: 786 
• Unique protein chains: 2

6C90

Human Mtr4 helicase in complex with ZCCHC8-CTD

• DOI: 10.2210/pdb6C90/pdb

• Classification: HYDROLASE/RNA binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-25 Released: 2018-05-30 
• Deposition Author(s): Puno, M.R., Lima, C.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex.

Puno, M.R., Lima, C.D.

(2018) Proc Natl Acad Sci U S A 115: E5506-E5515

• PubMed: 29844170 
• DOI: 10.1073/pnas.1803530115
• Primary Citation of Related Structures:  
  6C90


• PubMed Abstract: 
  

The nuclear exosome-targeting (NEXT) complex functions as an RNA exosome cofactor and is involved in surveillance and turnover of aberrant transcripts and noncoding RNAs. NEXT is a ternary complex composed of the RNA-binding protein RBM7, the scaffold zinc-knuckle protein ZCCHC8, and the helicase MTR4. While RNA interactions with RBM7 are known, it remains unclear how NEXT subunits collaborate to recognize and prepare substrates for degradation. Here, we show that MTR4 helicase activity is enhanced when associated with RBM7 and ZCCHC8. While uridine-rich substrates interact with RBM7 and are preferred, optimal activity is observed when substrates include a polyadenylated 3' end. We identify a bipartite interaction of ZCCHC8 with MTR4 and uncover a role for the conserved C-terminal domain of ZCCHC8 in stimulating MTR4 helicase and ATPase activities. A crystal structure reveals that the ZCCHC8 C-terminal domain binds the helicase core in a manner that is distinct from that observed for Saccharomyces cerevisiae exosome cofactors Trf4p and Air2p. Our results are consistent with a model whereby effective targeting of substrates by NEXT entails recognition of elements within the substrate and activation of MTR4 helicase activity.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Sloan Kettering Institute, New York, NY 10065.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome RNA helicase MTR4,Exosome RNA helicase MTR4	A	734	Homo sapiens	Mutation(s): 0  Gene Names: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens) Explore P42285  Go to UniProtKB:  P42285
NIH Common Fund Data Resources
PHAROS:  P42285 GTEx:  ENSG00000039123

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger CCHC domain-containing protein 8	B	52	Homo sapiens	Mutation(s): 0  Gene Names: ZCCHC8
Find proteins for Q6NZY4 (Homo sapiens) Explore Q6NZY4  Go to UniProtKB:  Q6NZY4
NIH Common Fund Data Resources
PHAROS:  Q6NZY4 GTEx:  ENSG00000033030

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
TLA	A	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
MLI	A	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.635	α = 90
b = 147.635	β = 90
c = 101.589	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-25 
• Released Date: 2018-05-30 
Deposition Author(s): Puno, M.R., Lima, C.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118080
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2018-06-20
  Changes: Data collection, Database references
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence