4ZXN | pdb_00004zxn

Crystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase

• PDB DOI: https://doi.org/10.2210/pdb4ZXN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rat coronavirus (strain NJ)
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-05-20 Released: 2016-05-11 
• Deposition Author(s): Bakkers, M.J.G., Feitsma, L.J., Huizinga, E.G., de Groot, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: other

Literature

Crystal structures of murine coronavirus hemagglutinin-esterases reveal structural basis for esterase substrate specificity

Bakkers, M.J.G., Feitsma, L.J., Huizinga, E.G., de Groot, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 45.03 kDa 
• Atom Count: 3,104 
• Modeled Residue Count: 369 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HE protein	A	388	Rat coronavirus (strain NJ)	Mutation(s): 1  Gene Names: HE EC: 3.1.1.53
UniProt
Find proteins for Q3HS77 (Rat coronavirus) Explore Q3HS77  Go to UniProtKB:  Q3HS77
Glycosylation
Glycosylation Sites: 6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.71	α = 90
b = 184.37	β = 90
c = 76.9	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Bakkers, M.J.G., Feitsma, L.J., Huizinga, E.G., de Groot, R.J.

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary