6MEN | pdb_00006men

Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate glucose (ADP-glucose)

• PDB DOI: https://doi.org/10.2210/pdb6MEN/pdb

• Classification: HYDROLASE
• Organism(s): Tylonycteris bat coronavirus HKU4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-06 Released: 2019-09-11 
• Deposition Author(s): Hammond, R.G., Schormann, N., McPherson, R.L., Leung, A.K.L., Deivanayagam, C.C.S., Johnson, M.A.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

ADP-Ribose and Analogues bound to the DeMARylating Macrodomain from the Bat Coronavirus HKU4

Hammond, R.G., Schormann, N., McPherson, R.L., Leung, A.K.L., Deivanayagam, C., Johnson, M.A.

(2021) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.2004500118

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.37 kDa 
• Atom Count: 2,739 
• Modeled Residue Count: 323 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	174	Tylonycteris bat coronavirus HKU4	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6W3 (Bat coronavirus HKU4) Explore P0C6W3  Go to UniProtKB:  P0C6W3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADQ	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE C16 H25 N5 O15 P2 WFPZSXYXPSUOPY-ROYWQJLOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.548	α = 73.04
b = 41.691	β = 88.37
c = 60.001	γ = 88.05

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Hammond, R.G., Schormann, N., McPherson, R.L., Leung, A.K.L., Deivanayagam, C.C.S., Johnson, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R35GM119456

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2021-01-13
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description