7CKM | pdb_00007ckm

Structure of Machupo virus polymerase bound to Z matrix protein (monomeric complex)

• PDB DOI: https://doi.org/10.2210/pdb7CKM/pdb
• EM Map EMD-30388: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Mammarenavirus machupoense
• 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: 3.37 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: 261.39 kDa 
• Atom Count: 13,114 
• Modeled Residue Count: 1,652 
• Deposited Residue Count: 2,303 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,209	Mammarenavirus machupoense	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for Q6IVU0 (Machupo virus) Explore Q6IVU0  Go to UniProtKB:  Q6IVU0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein Z	B	94	Mammarenavirus machupoense	Mutation(s): 0
UniProt
Find proteins for Q6UY77 (Machupo virus) Explore Q6UY77  Go to UniProtKB:  Q6UY77

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth B], G [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: 3.37 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: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary