7IBQ | pdb_00007ibq

PanDDA analysis group deposition -- SARS-CoV-2 Nsp1 crystal A10 (dataset 1) from the KIT library screening campaign, data used for ground state calculation

• PDB DOI: https://doi.org/10.2210/pdb7IBQ/pdb
• Deposition Group: G_1002337 (ground state) | Explore  G_1002337  

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-27 Released: 2025-10-22 
• Deposition Author(s): Lennartz, F., Weiss, M.S.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystallographic fragment screening against SARS-CoV-2 nonstructural protein 1 using the F2X-Entry Screen and a newly developed fragment library.

Lennartz, F., Wollenhaupt, J., Oelker, M., Froling, P., Mueller, U., Deckers, A., Grathwol, C., Brase, S., Jung, N., Weiss, M.S.

(2025) Acta Crystallogr D Struct Biol 81: 630-645

• PubMed: 41081353 
• DOI: https://doi.org/10.1107/S2059798325008563
• Primary Citation Related Structures: 
  7IB8, 7IB9, 7IBA, 7IBB, 7IBC, 7IBD, 7IBE, 7IBF, 7IBG, 7IBH, 7IBI, 7IBJ, 7IBK, 7IBL, 7IBM, 7IBN, 7IBO, 7IBP, 7IBQ, 7IBR, 7IBS, 7IBT, 7IBU, 7IBV, 7IBW, 7IBX, 7IBY, 7IBZ, 7IC0, 7IC1, 7IC2, 7IC3, 7IC4, 7IC5, 7IC6, 7IC7, 7IC8, 7IC9, 7ICA, 7ICB, 7ICC, 7ICW, 7ICX, 7ICY, 7ICZ, 7ID0, 7ID1, 7ID2, 7ID3, 7ID4, ... Search all related entries


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to threaten global health. This underpins the need for novel therapeutics against this virus. Nonstructural protein 1 (Nsp1) of SARS-CoV-2 is a multifunctional protein with an essential role in viral replication. As such, it presents itself as an attractive target for drug discovery. Here, we describe two crystallographic fragment-screening campaigns against Nsp1, one using the established F2X-Entry Screen and one using a new, chemically and structurally diverse fragment library, which we call the KIT library. Together, 21 hits could be identified from 192 screened fragments, which constitutes the highest hit rate reported for Nsp1 to date. Many hits bind to a key functional region and interact with residues involved in cellular mRNA cleavage, ribosome binding and viral RNA recognition. Furthermore, most of the identified fragments share a common binding mode, providing promising starting points for further optimization into drug-like compounds that can disrupt the role of Nsp1 in viral replication.

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Organizational Affiliation: 
• Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany.
Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131 Karlsruhe, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 12.86 kDa 
• Atom Count: 930 
• Modeled Residue Count: 113 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Host translation inhibitor nsp1	A	116	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.83	α = 90
b = 36.83	β = 90
c = 142.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data scaling
XDS	data reduction
xdsapp	data scaling
xdsapp	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Lennartz, F., Weiss, M.S.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references