+Open data
-Basic information
Entry | Database: PDB / ID: 6pik | ||||||
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Title | Tetrameric cryo-EM ArnA | ||||||
Components |
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Keywords | ANTIBIOTIC / Polymyxin resistance / hexamer / tetramer | ||||||
Function / homology | Function and homology information : / UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process ...: / UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli DH5[alpha] (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
Authors | Yang, M. / Gehring, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Cryo-electron microscopy structures of ArnA, a key enzyme for polymyxin resistance, revealed unexpected oligomerizations and domain movements. Authors: Meng Yang / Yu Seby Chen / Muneyoshi Ichikawa / Daniel Calles-Garcia / Kaustuv Basu / Rayan Fakih / Khanh Huy Bui / Kalle Gehring / Abstract: Gram-negative bacteria evade the attack of cationic antimicrobial peptides through modifying their lipid A structure in their outer membranes with 4-amino-4-deoxy-L-arabinose (Ara4N). ArnA is a ...Gram-negative bacteria evade the attack of cationic antimicrobial peptides through modifying their lipid A structure in their outer membranes with 4-amino-4-deoxy-L-arabinose (Ara4N). ArnA is a crucial enzyme in the lipid A modification pathway and its deletion abolishes the polymyxin resistance of gram-negative bacteria. Previous studies by X-ray crystallography have shown that full-length ArnA forms a three-bladed propeller-shaped hexamer. Here, the structures of ArnA determined by cryo-electron microscopy (cryo-EM) reveal that ArnA exists in two 3D architectures, hexamer and tetramer. This is the first observation of a tetrameric ArnA. The hexameric cryo-EM structure is similar to previous crystal structures but shows differences in domain movements and conformational changes. We propose that ArnA oligomeric states are in a dynamic equilibrium, where the hexamer state is energetically more favorable, and its domain movements are important for cooperating with downstream enzymes in the lipid A-Ara4N modification pathway. The results provide us with new possibilities to explore inhibitors targeting ArnA. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pik.cif.gz | 473.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pik.ent.gz | 389.1 KB | Display | PDB format |
PDBx/mmJSON format | 6pik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pik_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6pik_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6pik_validation.xml.gz | 77.5 KB | Display | |
Data in CIF | 6pik_validation.cif.gz | 107.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/6pik ftp://data.pdbj.org/pub/pdb/validation_reports/pi/6pik | HTTPS FTP |
-Related structure data
Related structure data | 20352MC 0456C 6pihC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 32717.416 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Gene: arnA, EIT12_05710 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A3W2RQG2, UniProt: P77398*PLUS, UDP-4-amino-4-deoxy-L-arabinose formyltransferase, UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) #2: Protein | Mass: 40057.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Gene: arnA, BvCmsC61A_03676 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A479JW67, UniProt: P77398*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ArnA / Type: COMPLEX / Details: Full length ArnA from E.coli / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.44 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli DH5[alpha] (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38127 / Symmetry type: POINT |