7BN3

Crystal structure of C-terminal domain of PABPC1 in complex with Nucleoprotein from Human Coronavirus 229E

• PDB DOI: https://doi.org/10.2210/pdb7BN3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Human coronavirus 229E
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-21 Released: 2022-03-02 
• Deposition Author(s): Badgujar, D.C., Dobritzsch, D.
• Funding Organization(s): The Swedish Foundation for Strategic Research, Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalic, F., Simonetti, L., Giudice, G., Sander, M.R., Lindqvist, R., Peters, M.B.A., Benz, C., Kassa, E., Badgujar, D., Inturi, R., Ali, M., Krystkowiak, I., Sayadi, A., Andersson, E., Aronsson, H., Soderberg, O., Dobritzsch, D., Petsalaki, E., Overby, A.K., Jemth, P., Davey, N.E., Ivarsson, Y.

(2023) Nat Commun 14

• DOI: https://doi.org/10.1038/s41467-023-38015-5

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

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

Macromolecule Content

• Total Structure Weight: 35.08 kDa 
• Atom Count: 2,253 
• Modelled Residue Count: 286 
• Deposited Residue Count: 327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Polyadenylate-binding protein 1	A, B, C	92	Homo sapiens	Mutation(s): 0  Gene Names: PABPC1, PAB1, PABP1, PABPC2
UniProt & NIH Common Fund Data Resources
Find proteins for P11940 (Homo sapiens) Explore P11940  Go to UniProtKB:  P11940
PHAROS:  P11940 GTEx:  ENSG00000070756

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein from Human Coronavirus 229E	D [auth F], E [auth D], F [auth E]	17	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for P15130 (Human coronavirus 229E) Explore P15130  Go to UniProtKB:  P15130

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B], H [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.509	α = 90
b = 150.065	β = 90
c = 65.502	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Badgujar, D.C., Dobritzsch, D.

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Funding Organization	Location	Grant Number
The Swedish Foundation for Strategic Research	Sweden	SB16-0039
Swedish Research Council	Sweden	2016-04965
Swedish Research Council	Sweden	2016-04134

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-05-10
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description