8tc3

From Proteopedia

CryoEM structure of nucleotide-free form of the nitrogenase iron protein from A. vinelandii

PDB ID 8tc3

Drag the structure with the mouse to rotate

Structural highlights

8tc3 is a 2 chain structure with sequence from Azotobacter vinelandii DJ and Discosoma sp. LW-2004. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.57Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5S3G7_9CNID NIFH1_AZOVI The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533]

Publication Abstract from PubMed

Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology. We have recently demonstrated the success of an anaerobic single-particle cryoEM workflow applied to the air-sensitive nitrogenase enzymes. In this protocol, we detail the use of Schlenk lines and anaerobic chambers to prepare samples, including a protein tag for monitoring sample exposure to oxygen in air. We describe how to use a plunge freezing apparatus inside of a soft-sided vinyl chamber of the type we routinely use for anaerobic biochemistry and crystallography of oxygen-sensitive proteins. Manual control of the airlock allows for introduction of liquid cryogens into the tent. A custom vacuum port provides slow, continuous evacuation of the tent atmosphere to avoid accumulation of flammable vapors within the enclosed chamber. These methods allowed us to obtain high-resolution structures of both nitrogenase proteins using single-particle cryoEM. The procedures involved can be generally subdivided into a 4 d anaerobic sample generation procedure, and a 1 d anaerobic cryoEM sample preparation step, followed by conventional cryoEM imaging and processing steps. As nitrogen is a substrate for nitrogenase, the Schlenk lines and anaerobic chambers described in this procedure are operated under an argon atmosphere; however, the system and these procedures are compatible with other controlled gas environments.

Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins.,Warmack RA, Wenke BB, Spatzal T, Rees DC Nat Protoc. 2024 Jul;19(7):2026-2051. doi: 10.1038/s41596-024-00973-5. Epub 2024 , Apr 4. PMID:38575747^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Warmack RA, Wenke BB, Spatzal T, Rees DC. Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nat Protoc. 2024 Jul;19(7):2026-2051. PMID:38575747 doi:10.1038/s41596-024-00973-5