8CNT | pdb_00008cnt

Structure of the DEAH-box helicase Prp16 in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb8CNT/pdb

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-24 Released: 2023-08-23 
• Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Prp16 in complex with ADP.

Garbers, T.B., Enders, M., Neumann, P., Ficner, R.

(2023) Acta Crystallogr F Struct Biol Commun 79: 200-207

• PubMed: 37548918 
• DOI: https://doi.org/10.1107/S2053230X23005721
• Primary Citation Related Structures: 
  8CNT


• PubMed Abstract: 
  

  DEAH-box helicases play a crucial role in pre-mRNA splicing as they are responsible for major rearrangements of the spliceosome and are involved in various quality-ensuring steps. Prp16 is the driving force during spliceosomal catalysis, remodeling the C state into the C* state. Here, the first crystal structure of Prp16 from Chaetomium thermophilum in complex with ADP is reported at 1.9 Å resolution. Comparison with the other spliceosomal DEAH-box helicases Prp2, Prp22 and Prp43 reveals an overall identical domain architecture. The β-hairpin, which is a structural element of the RecA2 domain, exhibits a unique position, punctuating its flexibility. Analysis of cryo-EM models of spliceosomal complexes containing Prp16 reveals that these models show Prp16 in its nucleotide-free state, rendering the model presented here the first structure of Prp16 in complex with a nucleotide.

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Organizational Affiliation: 
• Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.27 kDa 
• Atom Count: 5,396 
• Modeled Residue Count: 620 
• Deposited Residue Count: 633 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA splicing factor ATP-dependent RNA helicase prp16-like protein	A	633	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0009880 EC: 3.6.4.13
UniProt
Find proteins for G0S0F9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S0F9  Go to UniProtKB:  G0S0F9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.13	α = 90
b = 102.14	β = 90
c = 106.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 860, TP A02

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release