5W0M | pdb_00005w0m

Structure of human TUT7 catalytic module (CM) in complex with U5 RNA

• PDB DOI: https://doi.org/10.2210/pdb5W0M/pdb
• NAKB: 5W0M

• Classification: TRANSFERASE/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-05-31 Released: 2017-06-28 
• Deposition Author(s): Faehnle, C.R., Walleshauser, J., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis.

Faehnle, C.R., Walleshauser, J., Joshua-Tor, L.

(2017) Nat Struct Mol Biol 24: 658-665

• PubMed: 28671666 
• DOI: https://doi.org/10.1038/nsmb.3428
• Primary Citation Related Structures: 
  5W0B, 5W0M, 5W0N, 5W0O


• PubMed Abstract: 
  

  The uridyl transferases TUT4 and TUT7 (collectively called TUT4(7)) switch between two modes of activity, either promoting expression of let-7 microRNA (monoU) or marking it for degradation (oligoU). Lin28 modulates the switch via recruitment of TUT4(7) to the precursor pre-let-7 in stem cells and human cancers. We found that TUT4(7) utilize two multidomain functional modules during the switch from monoU to oligoU. The catalytic module (CM) is essential for both activities, while the Lin28-interacting module (LIM) is indispensable for oligoU. A TUT7 CM structure trapped in the monoU activity staterevealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins to favor monoU addition. Conversely, the switch to oligoU requires the ZK domain of Lin28 to drive the formation of a stable ternary complex between pre-let-7 and the inactive LIM. Finally, ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions.

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Organizational Affiliation: 
• W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 139.65 kDa 
• Atom Count: 9,325 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,182 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal uridylyltransferase 7	A, B, C	389	Homo sapiens	Mutation(s): 1  Gene Names: ZCCHC6, HS2, KIAA1711, TUT7 EC: 2.7.7.52
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VYS8 (Homo sapiens) Explore Q5VYS8  Go to UniProtKB:  Q5VYS8
PHAROS:  Q5VYS8 GTEx:  ENSG00000083223

Entity ID: 2
Molecule	Chains	Length	Organism	Image
U5 single-stranded RNA	D [auth H], E [auth I], F [auth J]	5	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	J [auth A], L [auth B], O [auth C], P [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	G [auth A], H [auth A], K [auth B], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth A], N [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.472	α = 90
b = 135.472	β = 90
c = 179.268	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Faehnle, C.R., Walleshauser, J., Joshua-Tor, L.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-19
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description