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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20352 | |||||||||
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Title | Tetrameric cryo-EM ArnA | |||||||||
![]() | Local sharpened tetrameric cryo-EM ArnA | |||||||||
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![]() | Polymyxin resistance / hexamer / tetramer / ANTIBIOTIC | |||||||||
Function / homology | ![]() : / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
![]() | Yang M / Gehring K | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.6 KB | Display | ![]() |
Images | ![]() | 33.7 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 26.1 MB 25.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 645.1 KB | Display | ![]() |
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Full document | ![]() | 644.7 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pikMC ![]() 0456C ![]() 6pihC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Local sharpened tetrameric cryo-EM ArnA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: The half map of tetrameric cryo-EM ArnA
File | emd_20352_half_map_1.map | ||||||||||||
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Annotation | The half map of tetrameric cryo-EM ArnA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The half map of tetrameric cryo-EM ArnA
File | emd_20352_half_map_2.map | ||||||||||||
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Annotation | The half map of tetrameric cryo-EM ArnA | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ArnA
Entire | Name: ArnA |
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Components |
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-Supramolecule #1: ArnA
Supramolecule | Name: ArnA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full length ArnA from E.coli |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 440 KDa |
-Macromolecule #1: Bifunctional polymyxin resistance protein ArnA
Macromolecule | Name: Bifunctional polymyxin resistance protein ArnA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO EC number: UDP-4-amino-4-deoxy-L-arabinose formyltransferase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 32.717416 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA ERGIPVYAPD NVNHPLWVER IAQLSPDVIF SFYYRHLIY DEILQLAPAG AFNLHGSLLP KYRGRAPLNW VLVNGETETG VTLHRMVKRA DAGAIVAQLR IAIAPDDIAI T LHHKLCHA ...String: MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA ERGIPVYAPD NVNHPLWVER IAQLSPDVIF SFYYRHLIY DEILQLAPAG AFNLHGSLLP KYRGRAPLNW VLVNGETETG VTLHRMVKRA DAGAIVAQLR IAIAPDDIAI T LHHKLCHA ARQLLEQTLP AIKHGNILEI AQRENEATCF GRRTPDDSFL EWHKPASVLH NMVRAVADPW PGAFSYVGNQ KF TVWSSRV HPHASKAQPG SVISVAPLLI ACGDGALEIV TGQAGDGITM QGSQLAQTLG LVQ UniProtKB: Bifunctional polymyxin resistance protein ArnA |
-Macromolecule #2: UDP-4-amino-4-deoxy-L-arabinose formyltransferase
Macromolecule | Name: UDP-4-amino-4-deoxy-L-arabinose formyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.057586 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRVLILGVNG FIGNHLTERL LREDHYEVYG LDIGSDAISR FLNHPHFHFV EGDISIHSEW IEYHVKKCDV VLPLVAIATP IEYTRNPLR VFELDFEENL RIIRYCVKYR KRIIFPSTSE VYGMCSDKYF DEDHSNLIVG PVNKPRWIYS VSKQLLDRVI W AYGEKEGL ...String: MRVLILGVNG FIGNHLTERL LREDHYEVYG LDIGSDAISR FLNHPHFHFV EGDISIHSEW IEYHVKKCDV VLPLVAIATP IEYTRNPLR VFELDFEENL RIIRYCVKYR KRIIFPSTSE VYGMCSDKYF DEDHSNLIVG PVNKPRWIYS VSKQLLDRVI W AYGEKEGL QFTLFRPFNW MGPRLDNLNA ARIGSSRAIT QLILNLVEGS PIKLIDGGKQ KRCFTDIRDG IEALYRIIEN AG NRCDGEI INIGNPENEA SIEELGEMLL ASFEKHPLRH HFPPFAGFRV VESSSYYGKG YQDVEHRKPS IRNAHRCLDW EPK IDMQET IDETLDFFLR TVDLTDKPS UniProtKB: Bifunctional polymyxin resistance protein ArnA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |