7CKL | pdb_00007ckl

Structure of Lassa virus polymerase bound to Z matrix protein

• PDB DOI: https://doi.org/10.2210/pdb7CKL/pdb
• EM Map EMD-30387: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Mammarenavirus lassaense
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-17 Released: 2021-05-05 
• Deposition Author(s): Xu, X., Peng, R., Peng, Q., Shi, Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals

Xu, X., Peng, R., Peng, Q., Wang, M., Xu, Y., Liu, S., Tian, X., Deng, H., Tong, Y., Hu, X., Zhong, J., Wang, P., Qi, J., Gao, G.F., Shi, Y.

(2021) Nat Microbiol 6: 921-931

• DOI: https://doi.org/10.1038/s41564-021-00916-w

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 264.43 kDa 
• Atom Count: 11,521 
• Modeled Residue Count: 1,464 
• Deposited Residue Count: 2,317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,218	Mammarenavirus lassaense	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for A0A097F4L1 (Mammarenavirus lassaense) Explore A0A097F4L1  Go to UniProtKB:  A0A097F4L1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein Z	B	99	Mammarenavirus lassaense	Mutation(s): 0
UniProt
Find proteins for A0A097F4I8 (Mammarenavirus lassaense) Explore A0A097F4I8  Go to UniProtKB:  A0A097F4I8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.17

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Xu, X., Peng, R., Peng, Q., Shi, Y.

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary